Starting phenix.real_space_refine
on Tue Jan 14 05:09:22 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      16      5.16       5
     C    3611      2.51       5
     N     967      2.21       5
     O    1112      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5712
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 439
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "H"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
    Chain: "V"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 120
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "A"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 849
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2596
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 21, 'TRANS': 304}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 800
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
  Time building chain proxies: 4.22, per 1000 atoms: 0.74
  Number of scatterers: 5712
  At special positions: 0
  Unit cell: (60.48, 122.4, 102.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       6     15.00
     O    1112      8.00
     N     967      7.00
     C    3611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS B 120 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 668.3 milliseconds
  

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 14 sheets defined
      4.0% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 4.088A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 64
      removed outlier: 3.520A  pdb=" N   LYS A  64 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 61 through 64'
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'B' and resid 98 through 109
    Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88
    Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 110
    Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 63
      removed outlier: 7.002A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   CYS H  99 " --> pdb=" O   GLN H 115 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   GLN H 115 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG H 101 " --> pdb=" O   TRP H 113 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TRP H 113 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'V' and resid 361 through 364
    Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 7
      removed outlier: 4.215A  pdb=" N   GLN A   5 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A  23 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.532A  pdb=" N   THR A 111 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   MET A  34 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   SER A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.875A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.819A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.875A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.819A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.538A  pdb=" N   VAL B 343 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.284A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.612A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.907A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)

    218 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.58 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1829
        1.34 -     1.46: 1411
        1.46 -     1.58: 2547
        1.58 -     1.70: 22
        1.70 -     1.82: 23
  Bond restraints: 5832
  Sorted by residual:
  bond pdb=" OG1 TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.606  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" OG1 TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" O3P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" O2P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" O2P TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.61e+01
  ... (remaining 5827 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 7839
        2.53 -     5.06: 68
        5.06 -     7.59: 8
        7.59 -    10.12: 4
       10.12 -    12.65: 2
  Bond angle restraints: 7921
  Sorted by residual:
  angle pdb=" CB  TPO V 359 "
        pdb=" OG1 TPO V 359 "
        pdb=" P   TPO V 359 "
      ideal   model   delta    sigma   weight residual
     119.31  106.66   12.65 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" CB  TPO V 360 "
        pdb=" OG1 TPO V 360 "
        pdb=" P   TPO V 360 "
      ideal   model   delta    sigma   weight residual
     119.31  107.34   11.97 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" OG1 TPO V 360 "
        pdb=" P   TPO V 360 "
        pdb=" O1P TPO V 360 "
      ideal   model   delta    sigma   weight residual
     100.43  109.72   -9.29 3.00e+00 1.11e-01 9.59e+00
  angle pdb=" CA  TYR B  63 "
        pdb=" C   TYR B  63 "
        pdb=" O   TYR B  63 "
      ideal   model   delta    sigma   weight residual
     119.08  122.16   -3.08 1.03e+00 9.43e-01 8.96e+00
  angle pdb=" OG1 TPO V 359 "
        pdb=" P   TPO V 359 "
        pdb=" O1P TPO V 359 "
      ideal   model   delta    sigma   weight residual
     100.43  109.32   -8.89 3.00e+00 1.11e-01 8.79e+00
  ... (remaining 7916 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3016
       17.83 -    35.66: 366
       35.66 -    53.49: 78
       53.49 -    71.32: 16
       71.32 -    89.15: 6
  Dihedral angle restraints: 3482
    sinusoidal: 1367
      harmonic: 2115
  Sorted by residual:
  dihedral pdb=" CA  VAL C 111 "
           pdb=" C   VAL C 111 "
           pdb=" N   ASN C 112 "
           pdb=" CA  ASN C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.42  -21.58     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CB  CYS C  95 "
           pdb=" SG  CYS C  95 "
           pdb=" SG  CYS B 120 "
           pdb=" CB  CYS B 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.95  -30.05     1      1.00e+01 1.00e-02 1.29e+01
  dihedral pdb=" CA  LEU B  79 "
           pdb=" C   LEU B  79 "
           pdb=" N   PHE B  80 "
           pdb=" CA  PHE B  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.58  -17.42     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 3479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 516
       0.029 -    0.058: 243
       0.058 -    0.087: 67
       0.087 -    0.116: 45
       0.116 -    0.144: 22
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" CB  VAL C 111 "
            pdb=" CA  VAL C 111 "
            pdb=" CG1 VAL C 111 "
            pdb=" CG2 VAL C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ASP H 111 "
            pdb=" N   ASP H 111 "
            pdb=" C   ASP H 111 "
            pdb=" CB  ASP H 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 890 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  16 "    0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO H  17 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO H  17 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H  17 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  44 "    0.040 5.00e-02 4.00e+02   6.04e-02 5.84e+00
        pdb=" N   PRO B  45 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 107 "    0.006 2.00e-02 2.50e+03   1.22e-02 2.99e+00
        pdb=" CG  TYR H 107 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 107 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 107 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 107 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 107 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 107 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 107 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1411
        2.79 -     3.32: 4562
        3.32 -     3.85: 8562
        3.85 -     4.37: 9874
        4.37 -     4.90: 18352
  Nonbonded interactions: 42761
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  36 "
            pdb=" O   ILE H  54 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER B  13 "
            pdb=" OD1 ASN B  15 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ALA B 263 "
            pdb=" OG  SER B 266 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   SER H  66 "
            pdb=" NH2 ARG H  70 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" ND2 ASN C 135 "
            pdb=" O   ARG B  76 "
     model   vdw
     2.328 3.120
  ... (remaining 42756 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.270
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   5832  Z= 0.296
  Angle     :  0.645  12.650   7921  Z= 0.318
  Chirality :  0.043   0.144    893
  Planarity :  0.005   0.066   1000
  Dihedral  : 16.428  89.153   2117
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 25.44 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.32), residues: 700
  helix:  1.19 (1.59), residues: 11
  sheet:  0.48 (0.32), residues: 294
  loop : -0.91 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.005   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.029   0.002   TYR H 107 
 ARG   0.007   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.659 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7548 (t80) cc_final: 0.7344 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2060
  time to fit residues: 24.8673
Evaluate side-chains
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 18 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.3180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.097865 restraints weight = 7918.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.25
r_work: 0.3168 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5832  Z= 0.154
  Angle     :  0.531   8.478   7921  Z= 0.277
  Chirality :  0.043   0.161    893
  Planarity :  0.004   0.038   1000
  Dihedral  :  4.284  21.438    810
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.80 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.32), residues: 700
  helix:  1.83 (1.76), residues: 11
  sheet:  0.81 (0.33), residues: 285
  loop : -0.89 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.004   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.013   0.001   TYR C  90 
 ARG   0.002   0.000   ARG H  90 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.604 
Fit side-chains
REVERT: B  110 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: B  232 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7881 (mttp)
REVERT: L   80 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8054 (mt0)
  outliers start: 17
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1926
  time to fit residues: 25.8935
Evaluate side-chains
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5728

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.118190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.097350 restraints weight = 7942.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 2.45
r_work: 0.2911 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5832  Z= 0.212
  Angle     :  0.534   8.675   7921  Z= 0.278
  Chirality :  0.042   0.137    893
  Planarity :  0.004   0.035   1000
  Dihedral  :  4.327  22.600    810
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.12 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.32), residues: 700
  helix:  1.53 (1.69), residues: 11
  sheet:  0.79 (0.32), residues: 296
  loop : -0.95 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.009   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.017   0.001   TYR C 136 
 ARG   0.003   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.626 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7358 (t80) cc_final: 0.6780 (t80)
REVERT: B  110 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: B  232 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7898 (mttt)
REVERT: B  244 PHE cc_start: 0.8816 (m-10) cc_final: 0.8590 (m-10)
REVERT: L   80 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7984 (mt0)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1933
  time to fit residues: 26.6810
Evaluate side-chains
  102 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS
B 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.094587 restraints weight = 8135.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.47
r_work: 0.2973 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5832  Z= 0.323
  Angle     :  0.595   8.957   7921  Z= 0.310
  Chirality :  0.044   0.138    893
  Planarity :  0.004   0.044   1000
  Dihedral  :  4.637  20.399    810
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 24.32 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.32), residues: 700
  helix:  1.15 (1.69), residues: 11
  sheet:  0.76 (0.32), residues: 296
  loop : -1.09 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.011   0.001   HIS C 122 
 PHE   0.015   0.002   PHE H 105 
 TYR   0.024   0.002   TYR C 136 
 ARG   0.008   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 85
  time to evaluate  : 0.644 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8768 (t80) cc_final: 0.8527 (t80)
REVERT: H  107 TYR cc_start: 0.7680 (t80) cc_final: 0.7244 (t80)
REVERT: B  110 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: B  232 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7768 (mttt)
REVERT: B  244 PHE cc_start: 0.8855 (m-10) cc_final: 0.8522 (m-10)
REVERT: L   80 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8132 (mt0)
  outliers start: 34
  outliers final: 24
  residues processed: 113
  average time/residue: 0.1938
  time to fit residues: 28.2553
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.5278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.096935 restraints weight = 7901.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.44
r_work: 0.2859 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5832  Z= 0.196
  Angle     :  0.526   8.555   7921  Z= 0.271
  Chirality :  0.042   0.142    893
  Planarity :  0.004   0.044   1000
  Dihedral  :  4.410  25.583    810
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 25.60 %
    Favored  : 69.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.31), residues: 700
  helix:  1.20 (1.71), residues: 11
  sheet:  0.85 (0.32), residues: 296
  loop : -1.08 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.016   0.001   TYR C 136 
 ARG   0.009   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.597 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8812 (t80) cc_final: 0.8557 (t80)
REVERT: H  107 TYR cc_start: 0.7392 (t80) cc_final: 0.6817 (t80)
REVERT: B  110 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: B  232 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7856 (mttp)
REVERT: B  244 PHE cc_start: 0.8814 (m-10) cc_final: 0.8584 (m-10)
REVERT: L   80 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8009 (mt0)
  outliers start: 29
  outliers final: 24
  residues processed: 107
  average time/residue: 0.2042
  time to fit residues: 27.7891
Evaluate side-chains
  106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0170
   chunk 52 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.118270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.097284 restraints weight = 7900.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.45
r_work: 0.3037 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5832  Z= 0.201
  Angle     :  0.527   8.596   7921  Z= 0.270
  Chirality :  0.042   0.139    893
  Planarity :  0.004   0.049   1000
  Dihedral  :  4.389  29.631    810
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 26.89 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.32), residues: 700
  helix:  1.23 (1.72), residues: 11
  sheet:  0.86 (0.32), residues: 296
  loop : -1.13 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.016   0.001   TYR C 136 
 ARG   0.010   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.660 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8832 (t80) cc_final: 0.8582 (t80)
REVERT: H  107 TYR cc_start: 0.7372 (t80) cc_final: 0.6822 (t80)
REVERT: B  110 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8085 (tm-30)
REVERT: B  232 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7860 (mttt)
REVERT: L   80 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7986 (mt0)
  outliers start: 30
  outliers final: 26
  residues processed: 108
  average time/residue: 0.1891
  time to fit residues: 26.3887
Evaluate side-chains
  107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.096700 restraints weight = 7893.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.45
r_work: 0.3000 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5832  Z= 0.237
  Angle     :  0.544   8.676   7921  Z= 0.281
  Chirality :  0.043   0.177    893
  Planarity :  0.004   0.054   1000
  Dihedral  :  4.486  32.000    810
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 26.25 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.32), residues: 700
  helix:  1.24 (1.72), residues: 11
  sheet:  0.84 (0.32), residues: 296
  loop : -1.17 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.018   0.001   TYR C 136 
 ARG   0.012   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.664 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8848 (t80) cc_final: 0.8605 (t80)
REVERT: H  107 TYR cc_start: 0.7417 (t80) cc_final: 0.6874 (t80)
REVERT: A   69 ILE cc_start: 0.8845 (tt) cc_final: 0.8620 (tt)
REVERT: B  110 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7988 (tm-30)
REVERT: B  232 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7878 (mttt)
REVERT: L   80 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7969 (mt0)
  outliers start: 34
  outliers final: 27
  residues processed: 110
  average time/residue: 0.2156
  time to fit residues: 29.9691
Evaluate side-chains
  111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.114795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.093723 restraints weight = 7965.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.44
r_work: 0.3026 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   5832  Z= 0.423
  Angle     :  0.664  10.530   7921  Z= 0.343
  Chirality :  0.047   0.169    893
  Planarity :  0.005   0.060   1000
  Dihedral  :  5.092  33.260    810
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.73 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.32), residues: 700
  helix:  1.16 (1.72), residues: 11
  sheet:  0.74 (0.33), residues: 284
  loop : -1.32 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.009   0.001   HIS C 122 
 PHE   0.019   0.002   PHE H 105 
 TYR   0.025   0.002   TYR C 136 
 ARG   0.012   0.001   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 84
  time to evaluate  : 0.647 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7854 (t80) cc_final: 0.7489 (t80)
REVERT: A   43 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8190 (mtpp)
REVERT: B  110 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: B  232 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7931 (mttt)
REVERT: L   80 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8174 (mt0)
  outliers start: 33
  outliers final: 26
  residues processed: 112
  average time/residue: 0.1841
  time to fit residues: 26.7251
Evaluate side-chains
  109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.094764 restraints weight = 7871.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.46
r_work: 0.3041 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5832  Z= 0.224
  Angle     :  0.554   8.621   7921  Z= 0.285
  Chirality :  0.043   0.215    893
  Planarity :  0.004   0.062   1000
  Dihedral  :  4.834  41.244    810
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 27.86 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.32), residues: 700
  helix:  1.25 (1.73), residues: 11
  sheet:  0.76 (0.32), residues: 296
  loop : -1.25 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 122 
 PHE   0.014   0.001   PHE A  29 
 TYR   0.019   0.001   TYR B  63 
 ARG   0.013   0.000   ARG L  25 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.706 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7613 (t80) cc_final: 0.7188 (t80)
REVERT: A   43 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8214 (mtpp)
REVERT: B  110 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: B  232 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7945 (mttt)
REVERT: L   80 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (mt0)
  outliers start: 29
  outliers final: 27
  residues processed: 108
  average time/residue: 0.2035
  time to fit residues: 28.5609
Evaluate side-chains
  110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0000
   chunk 25 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0570
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.3702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.120523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.099339 restraints weight = 7922.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 2.47
r_work: 0.2950 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5832  Z= 0.160
  Angle     :  0.517   8.558   7921  Z= 0.264
  Chirality :  0.042   0.170    893
  Planarity :  0.004   0.064   1000
  Dihedral  :  4.653  50.026    810
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 28.66 %
    Favored  : 67.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.31), residues: 700
  helix:  1.27 (1.71), residues: 11
  sheet:  0.85 (0.32), residues: 296
  loop : -1.20 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 HIS   0.006   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.018   0.001   TYR B  63 
 ARG   0.015   0.000   ARG L  25 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.612 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7369 (t80) cc_final: 0.6811 (t80)
REVERT: A   43 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8441 (mtpp)
REVERT: B  110 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: B  232 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7971 (mttt)
REVERT: L   80 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7821 (mt0)
  outliers start: 25
  outliers final: 21
  residues processed: 103
  average time/residue: 0.1937
  time to fit residues: 25.7410
Evaluate side-chains
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0370
   chunk 10 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.119241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.098096 restraints weight = 7985.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.48
r_work: 0.3037 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5832  Z= 0.200
  Angle     :  0.540   8.598   7921  Z= 0.276
  Chirality :  0.042   0.151    893
  Planarity :  0.004   0.062   1000
  Dihedral  :  4.796  53.088    810
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 28.34 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.31), residues: 700
  helix:  1.33 (1.73), residues: 11
  sheet:  0.80 (0.31), residues: 298
  loop : -1.19 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.011   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.017   0.001   TYR B  63 
 ARG   0.013   0.000   ARG L  25 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3008.04 seconds
wall clock time: 55 minutes 13.08 seconds (3313.08 seconds total)